The clocks are same across working/non-working.
Is it possible to bisect the commit that's causing hang for 4.8x ?

[c499ff71ff2a281366c6ec7a904c547d806cbcd1] usb: dwc3: core: re-factor init and
exit paths
This patch causes both the hang on reboot and the lsusb hang.

How to reproduce? Why don't we see this on x86 and TI boards? I'm
guessing this is failed bisection, as I can't see anything in that
commit that would cause reboot hang. Also, that code path is *NOT*
executed when you run lsusb.

I did some more tests with next-20161016. Reverting / commenting out
one part of your patch "solves" the lsusb hang, the reboot problem
and also the "debounce failed" message. [1]
Another "solution" is to call phy_power_off before phy_power_on. [2]
Disclaimer: I have no idea what I was doing ;-) These were just some
simple trial-and-error attempts that maybe help to find the real
cause of the problems.
[1]
diff --git a/drivers/usb/dwc3/core.c b/drivers/usb/dwc3/core.c
index 7287a76..5ef589d 100644
--- a/drivers/usb/dwc3/core.c
+++ b/drivers/usb/dwc3/core.c
@@ -724,6 +724,7 @@ static int dwc3_core_init(struct dwc3 *dwc)
/* Adjust Frame Length */
dwc3_frame_length_adjustment(dwc);

This looks like a PHY driver bug to me. Which PHY driver are you using?

The exynos5-usbdrd phy driver is used for exynos platforms.
Looks like something is not right with the phy driver even
after applying the phy_calibrate patches.
Michael, are you using the last set of patches for phy calibration [1]?
[1] https://lkml.org/lkml/2015/2/2/257.
Thanks
Vivek
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